Kick-off was pushed back by more than 30 minutes as Liverpool fans struggled to gain entry to Stade de France, eventually taking their places to see Jurgen Klopp's men control much of the proceedings.
But Madrid got the vital goal in the 59th minute when Vinicius tucked away his fourth of this season's competition from one of just four Blancos attempts.
Premier League runner-up Liverpool was denied by a string of superb saves from Courtois either side of that strike, and Carlo Ancelotti's side held on to lift the famous trophy for a 14th time – seven more than any other side.
Liverpool had started in confident mood after the delay and only failed to take the lead inside the opening 20 minutes courtesy of two fine stops from Courtois.
The Real Madrid goalkeeper got down quickly to keep out Mohamed Salah's instinctive effort, before he superbly pawed Sadio Mane's powerful strike on to the post.
Madrid thought they had taken the lead shortly before the interval when Karim Benzema stroked home after some slapstick defending from Liverpool, yet it was ruled out for offside against the France international – the decision confirmed by the video assistant referee (VAR) after a lengthy review.
Madrid was not to be denied just before the hour mark, however, when Vinicius stole in behind Trent Alexander-Arnold to turn in Federico Valverde's low ball across the penalty area.
Courtois made three vital saves from Salah inside the final 20 minutes – the last of which really caught the eye – capping a wonderful individual display to ensure Ancelotti's men claimed a record-extending triumph.